10-81393490-T-C

Variant names:

• chr10-81393490-T-C
• rs588517

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.918 in 152,242 control chromosomes in the GnomAD database, including 64,238 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.92 (64238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139613 AN: 152122 Hom.: 64178 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.904

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.913

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.918 AC: 139733 AN: 152242 Hom.: 64238 Cov.: 32 AF XY: 0.919 AC XY: 68412 AN XY: 74440

African (AFR) AF: 0.961 AC: 39950 AN: 41558

American (AMR) AF: 0.929 AC: 14197 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3168 AN: 3472

East Asian (EAS) AF: 0.954 AC: 4940 AN: 5176

South Asian (SAS) AF: 0.928 AC: 4464 AN: 4812

European-Finnish (FIN) AF: 0.929 AC: 9852 AN: 10608

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60109 AN: 68010

Other (OTH) AF: 0.913 AC: 1931 AN: 2114

Alfa AF: 0.897 Hom.: 207785

Bravo AF: 0.919

Asia WGS AF: 0.958 AC: 3328 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs588517; hg19: chr10-83153246;